用化学结构增强检索生成,让大模型更准预测分子性质。
MolE-RAG: Molecular Structure-Enhanced Retrieval-Augmented Generation for Chemistry

- 不需训练,通过检索文献、分子信息和相似分子来增强推理
- 分类任务ROC-AUC最高提升28个百分点,回归任务RMSE降低67%
- 适合想不用调参就提升分子性质预测效果的研究者
大语言模型在分子性质预测方面展现出潜力,但其对化学结构的推理能力仍受限,因为分子表示如SMILES与语言模型训练所依赖的自然语言存在显著差异。为弥合这一语义与化学知识鸿沟,我们提出MolE-RAG,一种无需训练、以分子为中心的检索增强生成框架,用于基于LLM的分子性质预测。该方法在每次预测时引入三种互补的推理上下文:检索到的化学文献、包含化合物别名、标识符、官能团注释及理化描述符的分子特定信息,以及从训练集中检索出的结构相似分子。我们在九项分子性质预测任务上评估了MolE-RAG,使用专有、化学领域专用及开源的LLM。在通用大模型上,相较于仅使用SMILES的基线,MolE-RAG在分类任务中最大提升28个百分点的ROC-AUC,回归任务中相对减少67%的RMSE。我们还发现,不同上下文源的效用因模型和任务而异,部分模型最受益于文本检索,部分则更依赖分子上下文或结构检索。结果表明,无需微调即可通过分子中心检索提升基于大模型的分子性质预测性能,并提供在推理阶段融合异构化学知识的灵活框架。
原文摘要 · Abstract (English)
Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained. To bridge this semantic and chemical knowledge gap, we propose MolE-RAG, a training-free, molecule-centric retrieval-augmented generation framework for LLM-based molecular property prediction. MolE-RAG augments each prediction with three complementary sources of inference-time context: retrieved chemistry literature, molecule-specific information including compound synonyms, identifiers, functional group annotations, and physicochemical descriptors, and structurally similar molecules retrieved from the training set. We evaluate MolE-RAG across nine molecular property prediction tasks using proprietary, chemistry-specialized, and open-source LLMs. Across general-purpose LLMs, MolE-RAG improves ROC-AUC by up to 28 percentage points on classification tasks and reduces regression RMSE by up to 67% relative to a SMILES-only baseline. We further find that the utility of each context source varies across models and tasks, with different models benefiting most from textual retrieval, molecular context, or structural retrieval. These results suggest that molecule-centric retrieval can improve LLM-based molecular property prediction without model fine-tuning while providing a flexible framework for integrating heterogeneous chemical knowledge at inference time.
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